DROP Met: Data Resources Of Plant Metabolomics

DROP Met, Data Resources Of Plant Metabolomics, is a repository and distribution site of the dataset obtained from our multiple MS-based metabolome analyses. Various kinds of datasets, ranging from raw fundamental data on analytical conditions to metabolic profiles of plant samples, are available to the public. We release some datasets in the raw, hoping that users in bioinformatics and metabolomics fields will develop novel algorithms and methodologies of metabolomics using our datasets. Please read Terms of Use carefully before using DROP Met.

Integrated strategy for unknown EI-MS identification using quality control calibration curve, multivariate analysis, EI-MS spectral database, and retention index prediction
About GC-MS data files analyzing six types of Chinese medicine Senkyu can be downloaded.
This repository also includes pooled QC (quality control) data files used for QC curve filtering.
Please cite Integrated strategy for unknown EI-MS identification using quality control calibration curve, multivariate analysis, EI-MS spectral database, and retention index prediction Teruko Matsuo, Hiroshi Tsugawa, Hiromi Miyagawa, Eiichiro Fukusaki
Contents NetCDF files (six different origins of Senkyu, n = 6; seven concentration ranges of QC samples, n = 4)
A novel method for single-grain-based metabolic profiling of Arabidopsis seed
About Yuji Sawada, Hirokazu Tsukaya, Yimeng Li, Muneo Sato, Kensuke Kawade, Masami Yokota Hirai
Please cite Metabolomics (Minor revision)
Contents Metadata.xlsx for datasets
Waters raw data (4 Experimental group, n = 12, Extraction solvent control = 5)
Test dataset for MS-DIAL 2.0 and MS-FINDER 2.0
About Three validation kits are prepared for the evaluation of MS-DIAL 2.0 and MS-FINDER 2.0.
(1) The validation of MS-DIAL chromatogram deconvolution for GC/MS data was performed by six raw data files from five major MS vendors.
(2) Software comparison of MS-DIAL against other alternative programs was performed by four raw data files.
(3) Software comparison of MS-FINDER against other alternative programs was performed by five EI-MS spectra.
The raw files except for Bruker Daltonics and Thermo Fisher Scientific (because of their contracts) can be downloaded.
Please cite Identifying biologically important metabolites by mass spectrometry-based cheminformatics
Zijuan Lai, Hiroshi Tsugawa, Gert Wohlgemuth, Matthew Mueller, Yuxuan Zheng, Atsushi Ogiwara, Sajjan Mehta, John Meissen, Kohei Takeuchi, Tobias Kind, Peter Beal, Masanori Arita, Oliver Fiehn
Contents 1. Dataset for the validation of MS-DIAL chromatogram deconvolution
2. Dataset for software comparison (for MS-DIAL 2.0)
3. Dataset for software comparison (for MS-FINDER 2.0)
Raw LC/MS/MS data of nine algal species
About We performed a lipidomic analysis of nine algal species in our paper (Nature Methods 12, 523-526, 2015).
Total 188 LC/MS/MS data sets including data independent acquisition, data dependent acquisition, positive ion mode, negative ion mode, blank samples, and quality controls, can be downloaded from this repository.
A part of these files is also managed in our DropMet as 'MS-DIAL demo files'.
Please cite H.Tsugawa et al (2015) MS-DIAL: data independent MS/MS deconvolution for comprehensive metabolome analysis. Nature Methods, 12, 523–526
Contents AB Sciex raw data (.wiff & .wiff.scan), SWATH, Negative ion mode.
AB Sciex raw data (.wiff & .wiff.scan), SWATH, Positive ion mode.
AB Sciex raw data (.wiff & .wiff.scan), IDA, Negative ion mode.
AB Sciex raw data (.wiff & .wiff.scan), IDA, Positive ion mode.
Test dataset for the regular expression of MS/MS spectra data
About A regular expression of tandem mass spectrometry (MS/MS) data was developed to search structurally similar metabolites and to describe spectral motifs for partial annotation and characterization of metabolite structure (See project homepage External Link.)
Please cite Regular expressions of MS/MS spectra for partial annotation of metabolite features (Submitted)
Contents MS/MS strings of MassBank dataset (Supplementary Data 1) and MS/MS strings of Arabidopsis (ATH) and rice (OSA) MS/MS spectra data.
Metabolome data across different growth stages and across under different stress conditions in Brachypodium distachyon and wheat
About Widely targeted metabolome analysis was performed at different growth stages (BBCH00 seed, BBCH03 seed, BBCH10 seed, BBCH10 leaf, BBCH11 leaf, and BBCH13 leaf) by using B. distachyon accessions (Bd21 and Bd3-1) and Chinese Spring wheat. Furthermore, another metabolome analysis was also conducted under stress conditions (2℃, 12℃, 32℃, 42℃, 100 mM NaCl and 500 mM NaCl) using plants at the BBCH15 stage.
Please cite Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops
Yoshihiko Onda, Kei Hashimoto, Takuhiro Yoshida, Tetsuya Sakurai, Yuji Sawada, Masami Yokota Hirai, Kiminori Toyooka, Keiichi Mochida, and Kazuo Shinozaki Proceedings of the Royal Society B (provisionally accepted)
Contents
MS-DIAL demo files
About Both data independent MS/MS acquisition (SWATH) and data dependent MS/MS acquisition (IDA) data sets is downloaded as the demo files of MS-DIAL. In order to use MS-DIAL program, the user has to convert the vendor's raw data to ABF file format. The demonstration for file convert can be performed via AB Sciex raw data sets (.wiff and .wiff.scan). The file converter is available at http://www.reifycs.com/english/AbfConverter/ External Link. If you want to demonstrate MS-DIAL itself, please use the converted files (.abf) from the below link. Also see MSDIAL quick start
Please cite Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops
Yoshihiko Onda, Kei Hashimoto, Takuhiro Yoshida, Tetsuya Sakurai, Yuji Sawada, Masami Yokota Hirai, Kiminori Toyooka, Keiichi Mochida, and Kazuo Shinozaki Proceedings of the Royal Society B (provisionally accepted)
Contents AB Sciex raw data (.wiff & .wiff.scan), SWATH, Negative ion mode.
ABF files of the raw data set, SWATH, Negative ion mode.
AB Sciex raw data (.wiff & .wiff.scan), IDA, Negative ion mode.
ABF files of the raw data set, IDA, Negative ion mode.
Japanese rice 188 cultivars LC-MS dataset
About The metabolome data (NetCDF format, 188 cultivars * 4 replicates = 752 files) were obtained from 188 accessions of Japanese rice collection by liquid chromatography-tandem mass spectrometry (LC-MS/MS).
Please cite Matsuda et al. Submitted.
Contents
Untargeted metabolome data during drought stress in Arabidopsis thaliana
About The MS and MS/MS data of A. thaliana (Col-0) were acquired in positive mode of LC-QTOF-MS. The raw files were converted to netCDF and text files stored here.
Please cite Alternation of flavonoid accumulation under drought stress in Arabidopsis thaliana.
Ryo Nakabayashi, Tetsuya Mori, Kazuki Saito
Plant Signaling & Behavior External Link
Contents DAD 0
DAD 3
DAD 5
Metabolome data in Oryza sativa L. cultivar Habataki and MS/MS spectra of isolated compounds from rice leaves
About The MS/MS raw data were acquired in positive and negative mode of LC-QTOF-MS.
Please cite Toward better annotation in plant metabolomics: Isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses
Zhigang Yang, Ryo Nakabayashi, Yozo Okazaki, Tetsuya Mori, Satoshi Takamatsu, Susumu Kitanaka, Jun Kikuchi, Kazuki Saito
Metabolomics External Link
Contents
High resolution MS/MS spectra from health-promoting crops
About We collected MS/MS spectra from health-promoting crops by LC-QTOF-MS.
All data and metadata are freely available.
Contact person Ryo Nakabayashi
Acknowledgements This project was supported by Japan Advanced Plant Science Network and Strategic International Research Cooperative Program (SICP), JST.
Contents Allium cepa from Hokkaido Pref
Allium cepa from Saga Pref
Allium cepa (Early Red)
Allium sativum
Allium fistulosum (Bannounegi)
Asparagus officinalis
Brassica oleracea
Brassica rapa
Lactuca sativa
Raphanus sativus (peel of root)
Raphanus sativus (root)
Solanum tuberosum (peel of bulb)
Solanum tuberosum (bulb)
Wasabia japonica (root)
Wasabia japonica (leaf and stem)
Development of Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO)
About We chose 50 Arabidopsis mutants including a set of characterized and uncharacterized mutants, which resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry (GC-MS). All data are available for download in netCDF format.
MetaboLights ID: MTBLS47 External Link.
Please cite Metabolomic Characterization of Knock-Out Mutants in Arabidopsis - Development of a Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO) Atsushi Fukushima, Miyako Kusano, Ramon Francisco Mejia, Mami Iwasa,Makoto Kobayashi, Naomi Hayashi, Akiko Watanabe-Takahashi, Tomoko Narisawa, Takayuki Tohge, Manhoi Hur, Eve Syrkin Wurtele, Basil J.Nikolau, Kazuki Saito
Plant Physiology External Link
Contents
Metabolome data in Allium plants and MS/MS spectra of S-containing compounds
About The MS raw data were acquired in the positive mode of LC-FTICR-MS.
The raw files were converted to netCDF files stored here.
Please cite Submitted.
Contents
Metabolome data in Arabidopsis mutants overaccumulating and lacking flavonoids
About The MS raw data of the Arabidopsis mutants were acquired in positive mode of LC-QTOF-MS.
The raw files were converted to netCDF files stored here.
Please cite Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids
Ryo Nakabayashi, Keiko Yonekura-Sakakibara, Kaoru Urano, Makoto Suzuki, Yutaka Yamada, Tomoko Nishizawa, Fumio Matsuda, Mikiko Kojima, Hitoshi Sakakibara, Kazuo Shinozaki, Anthony J. Michael, Takayuki Tohge, Mami Yamazaki, Kazuki Saito
The Plant Journal External Link
Contents Unstress condition
Drought stress
Metabolic profile data of RILs of G. max and G. soja
About LC-ESI-QqQ-MS (UPLC-TQS, Waters) data derived from 93 Soybean RILs with excel file.
Please cite Computational and Structural Biotechnology Journal 2013
Yuji Sawada, Masami Yokota Hirai
Integrated LC-MS/MS system for plant metabolomics External Link
Contents
12C- & 13C-based metabolome data in onion bulb
About The MS and MS/MS raw data were acquired in the positive mode of LC-FT-ICR-MS.
The raw files were converted to netCDF files stored here.
Please cite Combination of Liquid Chromatography-Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry with 13C labeling for Chemical Assignment of Sulfur-containing Metabolites in Onion Bulbs
Ryo Nakabayashi, Yuji Sawada, Yutaka Yamada, Makoto Suzuki, Masami Yokota Hirai, Tetsuya Sakurai, and Kazuki Saito
Analytical Chemistry External Link
Contents
Metabolic profile data of LjMG RILines
About Total 88 metabolites of raw LC-ESI-QqQ-MS (UPLC-TQS, Waters) data derived from 132 LjMG RILines with excel file.
Metabolic profile data of LjMG RILines External Link
Please cite RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database.
Phytochemistry External Link
Contents
AtMetExpress 20 ecotypes raw LC-ESI-TOF-MS dataset
About Total 200 raw LC-ESI-TOF-MS chromatogram data derived from 20 Arabidopsis accession recorded with NetCDF format. These are part of the AtMetExpress metabolite accumulation atlas. Detailed information of each data files are described in the meta information (.txt) by following Metabolome Standard Initiative (MSI) recommendation.
Please cite Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity.
Front. Plant Sci. 2:40 (2011). doi: 10.3389/fpls.2011.00040 External Link
Contents
Exploring matrix effects and quantification performance in metabolomics experiments using artificial biological gradients
About Aritifical biological gradients between leaft and fruit samples from tomato for broad evaluation of quantification performance.
Please cite Exploring matrix effects and quantification performance in metabolomics experiments using artificial biological gradients. Redestig H, Kobayashi M, Saito K, Kusano M.
Anal Chem. 2011 Jun 1. External Link
Contents
Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment
About Metabolic profile data of miraculin over-expressing tomatoes grown on hydroponics (HC) and soil.
Please cite Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment. Kusano M, Redestig H, Hirai T, Oikawa A, Matsuda F, Fukushima A, Arita M, Watanabe S, Yano M, Hiwasa-Tanas K, Ezura H & Saito K.
PLoS ONE, 2011 External Link
Contents
  • File
  • Soil
  • zip archive: 1.9MB
Metabolite accumulation in seeds of Arabidopsis transposon-tagged mutants and accessions
About Metabolic profiles in seeds of 2,656 Arabidopsis transposon-tagged mutants and 225 Arabidopsis accessions. Peak areas were measured by UPLC-ZQMS analysis for 36 metabolites and recorded with Tab Separated Variables format.
Please cite Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources.
Journal of Plant Research. (2010) 123, 291–298 External Link
Contents
AtMetExpress Development raw LC-ESI-TOF-MS dataset
About Total 288 raw LC-ESI-TOF-MS chromatogram data derived from 36 Arabidopsis tissues recorded with NetCDF format. These are part of the AtMetExpress metabolite accumulation atlas. Detailed information of each data files are described in the meta information (.txt) by following Metabolome Standard Initiative (MSI) recommendation.
Please cite AtMetExpress Development: A phytochemical Atlas of Arabidopsis Develpment
Plant Physiol. (2010) in press. External Link
Contents
Mixture Dilution Series for Pre-processing Validation
About Total of 27 chromatograms with replicates of three different standard mixtures. Provided for validation of the Bioconductor package TargetSearch External Link
Please cite TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.
BMC Bioinformatics. (2009) 10:428 External Link
Contents
Metabolic profile data of Arabidopsis four aerial tissues
About Total 32 raw LC-ESI-MS chromatogram data derived from four Arabidopsis tissues (flower, rosette leaf, cauline leaf, and internode, eight replicates) recorded with NetCDF and ASCII format. Detailed information of each data files are described in the meta information (.txt) by following Metabolome Standard Initiative (MSI) recommendation. For details, please refer LC-MS branch.
Please cite MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites.
Plant J (2009) 57,555–577 External Link
Contents
Widely targeted metabolomics datasets ver 1.0
About We optimized multiple reaction monitoring (MRM) conditions to detect each of the 860 compounds (as of Mar 2009) by means of widely targeted metabolomics. All datasets useful to condition your measurement system are released here. ESI-MS/MS spectra are also available in ReSpect for Phytochemicals. A dataset of the metabolite accumulation patterns in 14 plants from Brassicaceae, Gramineae and Fabaceae is also released here.
Please cite Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants.
Plant Cell Physiol. (2009) 50, 37–47 [PubMed] External Link
Contents
 
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